Ensembits is the first tokenizer of protein conformational ensembles that outperforms static tokenizers on RMSF prediction and matches them on function and mutation tasks while using less pretraining data.
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citing papers explorer
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ENSEMBITS: an alphabet of protein conformational ensembles
Ensembits is the first tokenizer of protein conformational ensembles that outperforms static tokenizers on RMSF prediction and matches them on function and mutation tasks while using less pretraining data.
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Latent Process Generator Matching
Presents a general framework for generator matching on projected image spaces from latent Markov processes, generalizing static latent results to dynamic conditional processes.
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Entropy Across the Bridge: Conditional-Marginal Discretization for Flow and Schr\"odinger Samplers
Derives a conditional-marginal entropy-rate objective for bridge-aware discretization that yields U-shaped schedules and improves low-NFE sample quality on 2D, CIFAR-10, and protein tasks.
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From Mechanistic to Compositional Interpretability
The paper introduces compositional interpretability as a category-theoretic framework that casts mechanistic explanations as commuting syntactic-semantic mappings optimized under faithfulness and complexity constraints derived from minimum description length.
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ProteinJEPA: Latent prediction complements protein language models
Masked-position MLM plus JEPA latent prediction outperforms MLM-only pretraining on 10-11 of 16 downstream tasks for 35M-150M protein models while JEPA alone fails.
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TCD-Arena: Assessing Robustness of Time Series Causal Discovery Methods Against Assumption Violations
TCD-Arena is a new customizable testing framework that runs millions of experiments to map how 33 different assumption violations affect time series causal discovery methods and shows ensembles can boost overall robustness.
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Early-Exit Graph Neural Networks for Link Prediction
Early-exit GNNs for link prediction move the speed-quality Pareto frontier on the HeaRT benchmark by allowing implicit early exiting without auxiliary losses.
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Flexible Kernels for Protein Property Prediction
New class of sequence kernels for Gaussian processes that use substitution matrices and local linearity to enable data-efficient prediction of protein properties, with extensions to structure-aware multi-task learning.
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Towards Understanding Self-Pretraining for Sequence Classification
Self-pretraining improves Transformer sequence classification by enabling learning of proximity-biased attention from positional encodings that label supervision alone cannot easily acquire from random starts.
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CrystalBoltz: End-to-End Protein Structure Determination via Experiment-Guided Diffusion for X-Ray Crystallography
CrystalBoltz performs experiment-guided posterior sampling with diffusion models on structure-factor amplitudes for protein structure determination, reporting lower RMSD and R-factors than baselines with 33x faster runtime.
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Flashlight: PyTorch Compiler Extensions to Accelerate Attention Variants
Flashlight is a compiler-native PyTorch framework that generates efficient fused kernels for arbitrary and data-dependent attention variants, supporting more cases than FlexAttention with competitive performance.
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Improving Inverse Folding for Peptide Design with Diversity-regularized Direct Preference Optimization
Diversity-regularized DPO fine-tuning of ProteinMPNN improves structural similarity scores by at least 8% over base model and sequence diversity by up to 20% over standard DPO for peptide inverse folding on OpenFold structures.
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HSAP: A Hierarchical Sequence-aware Parallelism for Hybrid-Context Generative Models
HSAP introduces a hierarchical framework and sequence-aware algorithm with JIT-optimized NCCL communication to enable correct causal attention computation on hybrid-context packed sequences without limiting parallelism.
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Instrumented data for causal scientific machine learning
Instrumented data augments observations with mechanistic models, uncertainty, and counterfactuals to enable causal interventions via Pearl's do-operator in scientific machine learning.
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MOSAIC: Efficient Mixture-of-Agent Scheduling via Adaptive Aggregation and Inference Concurrency
MOSAIC uses an Integer Linear Program scheduler for expert placement and prompt assignment plus adaptive aggregation to achieve 1.7-2.3x end-to-end speedup on 4-GPU MoA workloads while keeping accuracy within 0.1pp.
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Sampling Parallelism for Fast and Efficient Bayesian Learning
Sampling parallelism distributes Bayesian sample evaluations across GPUs for near-perfect scaling, lower memory use, and faster convergence via per-GPU data augmentations, outperforming pure data parallelism in diversity.